I wonder if we have treated this "category" of sites entirely consistently

E.g "The Ruins of Jiaohe Ancient City" doesn't appear in China's "Former TWHS" list because it is regarded as having been subsumed within the greater "Silk Road" inscription
BUT "Burana Minaret" appears in Kyrgyzstan's list of "Former TWHS" even though it too has been fully included within the Silk Road inscription
Is this because China did at least "try" to gain an inscription for Jiaohe alone whilst Kyryzstan never attempted with Burana? If so I am not sure the logic holds

Similarly "Spoleto and Tempietto sul Clitunno" appears on Italy's list of "Former TWHS" even though the "Tempietto sul Clitunno" element was included in the Langobards inscription. The "History" of that WHS refers to Clitunno being added but the entry in the "Former TWHS list doesn't mention that the Clitunno element got inscribed (By the way Els - Spoleto of course as such didn't get inscribed even though the WHS description for the Langobards implies that it did "in full"! Presumably it only refers to the Basilica of San Salvatore in Spoleto)
There may be others??

That Burana Minaret is still included in the former TWHS although subsumed is a mistake.

The reason Spoleto and Tempietto sul Clitunno is still there is, as Solivagant duly noticed, that not all of Spoleto has been inscribed. Maybe it would be helpful to have an attached comment about the inscription of a part of it. Examples of similar cases are relatively common:
prehistoric sites (Israel), prehistoric sites (Cyprus), Olomouc (Czechia), Kezmarok (Slovakia), Cefalu (Italy), Cividale (Italy), Gargano (Italy), Piedmont vineyards with Valtellina (Italy), Palermo with botanic garden (Italy), Thessaloniki including ancient monuments (Greece), Athens (Greece) Franciscan monasteries of NE Brasil (Brasil), Malpelo and Gorgona (Colombia), Isfahan (Iran), Oaxaca with Cuilapan (Mexico), Puebla with Cholula (Mexico), Nan Madol with Lelu (Micronesia) and Pecs (Hungary).
I am pretty sure I missed some.

Perhaps in Former TWHS is a better location to post these retracted nominations.

Removed from Russia's Tentative List (6)
- The architectural and historical complex "Shelter of count N.P. Cheremetev" 1996
- The Valamo archipelago 1996
- Cathedral of Christ the Saviour 1998
- Church of Prince Dimitri "On Blood" 2001
- Russian Kremlins 2010
- Architectural and Park Ensemble "Tsar's Country Estate Izmaylovo" 2011

Removed from Cabo Verde's Tentative List (4)
- Cova e Montantes de Ribeiras da Torre et do Paul 2004
- La Saline de Pedra Lume 2004
- Le Plateau de la ville de Praia 2004
- Ville de Sao Filipe 2004

Renominated: Camp de concentration de Tarrafal 2004 (now 2016)

Removed from Lebanon Tentative List
- CENTRE HISTORIQUE DE TRIPOLI / MINA

Missing Azerbajan Tentative Sites
"Baku Stage" Mountain (30/09/1998)
"Binegadi" 4th Period Fauna and Flora Deposit (30/09/1998)

Changed it, thanks winterkjm

I found some misateks on the German site.
Former Tentative Sites
Bayreuth Festspielhaus
Caves with the oldest Ice Age art
The Bauhaus and associated sites in Weimar, Dessau and Bernau

Have all been inscribed already!

Wilhemshöhe:
Gardens and mansions in and around Kassel (including Friedrichplatz and Schloss Wilhelmsthal in Calden)
Great Spas of Europe: 16 baths were nominated now only 3 left in Germany, the rest is former tentative sites.

https://de.wikipedia.org/wiki/Welterbe_in_Deutschland
Website has all old nominations!

The Festspielhaus has NOT been "inscribed already" - only Beyreuth's "other" Opera House! The "Wiki" site you link to does state that it was Tentative from 1984 - 1993 (though for some strange reason it shows it in a different format from other "Former T List" sites.)

Regarding the change in number of baths in the continuing T List entry (now up for nomination of course) - we haven't normally shown such "small" changes in the definition of T List sites as justifying defining them as "Former" sites - it is still there as "Great Spas of Europe", albeit with changes. We could I guess track the changes Els?? Or might as well wait until the WHC now?

Yes, we wait.

The other 2 were shown accidentally (to keep a track record of 2017 nominations), I've now removed them and will look at the 2017 nominations of other countries.

From the top of my head:

Italie Area Archeologica di Saepinum e tratturi - thought we had it, missing indeed
Italie Contesti lacustri: S.Giulio, Isole Borromee e Villa Taranto a Pallanza - Lake Maggiore TWHS
Italie Parco Archeologico dell'Appia Antica - Via Appia TWHS
Italie Sacra di San Michele - CL of Benedictines TWHS
Italie Ville della nobilta' pontificia nel Lazio - Villas of Papal nobility TWHS
Slovaquie Breakthrough of the Dunajec River - Natural and cultural Danube region TWHS

http://whc.unesco.org/archive/1998/whc-98-conf203-9e.pdf
Espagne Casco histórico de Plasencia - Plasencia, Monfrague, Trujillo TWHS
Espagne La Ruta del vino y la cultura en los pueblos mediterráneos, La Rioja - La Rioja wine CL TWHS
Espagne Via de la plata, Extremadura - The silver rout TWHS

http://whc.unesco.org/archive/1999/whc-99-conf204-6e.pdf
Espagne Conjunto fortificado de Pamplona - Bulwarked fortification TWHS (although missing from history)
Espagne Conjunto Monumental de las Salinas de Añana, Alava-Araba - Vale salado de ANana TWHS
Espagne El parque etnológico de Torre del Ram, Punta Nati y ses Truquerias, Ciudadela. Menorca - Talayotic culture of Minorca TWHS
Espagne Ensemble arquéologique d'Ampurias - Greek archaeological ensemble in Ampuries TWHS
Espagne Ensemble du bourg de Morella - already there - Ciudad de Morella
Espagne Ensemble historique de la ville - Ciudad Rodrigo - Bulwarked fortification TWHS
Espagne Ensemble historique de la ville de Arcos de la Frontera - Monastery Santa Maria de la Rabida und the Columbus memorial places TWHS
Espagne Ensemble historique du bourg - Miranda del Castañar (Salamanque) - already there
Espagne Ensemble historique du bourg - Santillana del Mar - already there
Espagne Ermitage de San Baudelio de Berlanga - already there, albeit with a wrong name (BerlanDa)
Espagne Las Cañadas de La Mesta, Castilla-León - Mesta livestock trail TWHS
Espagne Las Herrerias [Almeria] - Mining historical heritage TWHS
Espagne Massif des Ancares - Ancares Someido TWHS
Espagne Molinos de viento del Campo de Cartagena - Mediterranean wind mills TWHS
Espagne Palais Royal [Madrid] - already there
Espagne Parc Naturel de Monfragüe - Plasencia, Monfrague, Trujillo TWHS
Espagne Pont romain d'Alcantara - Roman ways TWHS
Espagne Quartier historique de Trujillo - Plasencia, Monfrague, Trujillo TWHS
Espagne Ribeira Sacra - TWHS
Espagne Rodalquilar - Mining heritage TWHS
Espagne Ruta colombina - Monastery Santa Maria de la Rabida und the Columbus memorial places TWHS
Espagne Salon du Prado, Musée des Sciences et Jardin Botanique - Site of the Retiro and Prado TWHS
Mexique Système de Monastères du XVIe siècle au nord de l'état de Morelos - Popocatapetl monasteries WHS

TBC

Espagne Monastery of Sant Pere de Rodes
I see that we have this as having been encompassed within "The Mediterranean Facet of the Pyrenees (France-Spain)"
https://www.worldheritagesite.org/tentative/id/1986
It is certainly in the same general area but the description of "The Mediterranean Facet etc" is so lacking in detail and makes NO mention of any monastery that I am not sure on what basis we came to that conclusion.

So - we have so far only identified 3 additional missing "Former TWHS" - it certainly looks as if the majority on jonathonfr's list have been covered and "explained" and are not in fact "missing" - but that there are a few "unexplained" missing ones
Italy - Area Archeologica di Saepinum e tratturi
US - Denali
US - Trinity

I don't see it on the current indicative list, it's not in "Site of the Retiro and the Prado in Madrid"

It's there as a FTWHS: Madrid - Palacio Real.

Italie Insediamenti rupestri (Puglia) - Karstic caves in prehistoric Apulia TWHS
Italie Parco Archeologico Urbano e colline metallifere (Volterra) - Volterra TWHS
Italie Parco Nazionale della Calabria - Parco nazionale della Sila TWHS, but only partially, as it initially also included Parco nazionale all'Aspromonte
Italie Residenza Papale e quartiere San Pellegrino - Villas of Papal nobility TWHS
Italie Stagni e siti archeologici del Golfo di Oristano, Isola Maluventu - Ponds in the bay of Oristano TWHS

http://whc.unesco.org/archive/2007/whc07-31com-8af.pdf
Chine Beihai Park - The central axis of Beijing TWHS
Chine Songshan Area
Chine The Ancient Town of Tongli
Chine The Ancient Town of Zhouzhuang - The ancient waterfron towns in the south of Yangtze River TWHS
Chine The Ancient Venetian Township in the South of Yangtze River - Luzhi - same
Chine The Ancient Venetian Township in the South of Yangtze River - Nanxun - same
Chine The Ancient Venetian Township in the South of Yangtze River - Wuzhen - same
Chine The Ancient Venetian Township in the South of Yangtze River - Xitang - same
Chine The City Wall of Xian - Silk Roads WHS (although missing in history)
Chine The Remains of Chang'an City of the Han Dynasty - Silk Roads WHS
Chine The Ruins of Daming Palace of the Tang Dynasty - Silk Roads WHS
États-Unis d'Amérique Aleutian Islands Unit of the Alaska Maritime National Wildlife Refuge - Aleutian Islands TWHS
États-Unis d'Amérique Frank Lloyd Wright Home and Studio - Frank Lloyd TWHS
États-Unis d'Amérique Gates of the Artic National Park - Water Glacier International Park WHS
États-Unis d'Amérique Glacier National Park - Waterton Glacier International Park WHS
États-Unis d'Amérique Katmai National Park

Somewhat confusingly the Frank Lloyd Wright Home and Studio isn't part of the current FLW TWHS so should be treated as a separate entity.

It's in Alaska, not in Montana

Rather here:
http://whc.unesco.org/fr/listesindicatives/5324/